ptCoords: Getting and setting point coordinates

In Racmacs: Antigenic Cartography Macros

Getting and setting point coordinates

Description

Getting and setting of antigen and serum coordinates in a map optimization run (by default the currently selected one).

Usage

agCoords(map, optimization_number = 1)

srCoords(map, optimization_number = 1)

ptCoords(map, optimization_number = 1)

ptCoords(map, optimization_number = 1) <- value

agCoords(map, optimization_number = 1) <- value

srCoords(map, optimization_number = 1) <- value

Arguments

map	The acmap object
optimization_number	The optimization number from which to get / set the coordinates
value	A matrix of new coordinates to set

Details

These functions get and set point coordinates in a map. By default these coordinates refer to the currently selected optimization run, unless otherwise specified through the optimization_number argument.

99\ want to use but you should note that the outputs are actually the map base coordinates after the transformation and translation associated with the optimization run has been applied (see mapTransformation() and mapTranslation() for more details). When you set the antigen or serum coordinates through these functions, the transformed coordinates are "baked" in and the map transformation and translation are reset. Consequently if you want to apply a transformation to all coordinates generally, you are better off modifying the map translation and transformation directly, as is done by functions like rotateMap() and translateMap().

Value

Returns a matrix of point coordinates.

See Also

agBaseCoords() srBaseCoords() mapTransformation() mapTranslation()

Other map optimization attribute functions: colBases(), mapComment(), mapDimensions(), mapStress(), mapTransformation(), ptBaseCoords()

Racmacs documentation built on June 22, 2024, 11:33 a.m.